Initiate the script
Analyze DSRCT-specific genes in the samples
Identify tumor and normal cells
Briefly describe the general approach you took to achieve this goal.
Assessed gene expression in the cells
Used a z-score to determine tumor vs normal where z-score >0 is a tumor cell
It did not work well and we will try alternative methods
If known, do you anticipate filing additional pull requests to complete this analysis module?
Yes. I will add additional pull requests to use SingleR or similar method and signature based method like AUC.
Results
Delete this section if no results are associated with your pull request.
In this section, tell reviewers about what kinds of results (if any) your code produces.
Hi there, thanks for your contribution! Please fill out this template to help us review your code.
Remember, the more context you provide, the faster the review will go! For more information about filling out this template, please see the OpenScPCA documentation on filing pull requests: https://openscpca.readthedocs.io/en/latest/contributing-to-analyses/creating-pull-requests/
Before filing the pull request, you can also feel free to delete the italicized instruction lines in this template.
Purpose/implementation Section
In this section, tell reviewers about the scope and purpose of the code in the pull request.
Please link to the GitHub issue that this pull request addresses.
https://github.com/AlexsLemonade/OpenScPCA-analysis/issues/701 If applicable, you can also link to the associated GitHub Discussion. https://github.com/AlexsLemonade/OpenScPCA-analysis/discussions/583
What is the goal of this pull request?
Initiate the script Analyze DSRCT-specific genes in the samples Identify tumor and normal cells
Briefly describe the general approach you took to achieve this goal.
Assessed gene expression in the cells Used a z-score to determine tumor vs normal where z-score >0 is a tumor cell It did not work well and we will try alternative methods
If known, do you anticipate filing additional pull requests to complete this analysis module?
Yes. I will add additional pull requests to use SingleR or similar method and signature based method like AUC.
Results
Delete this section if no results are associated with your pull request.
In this section, tell reviewers about what kinds of results (if any) your code produces.
What is the name of your results bucket on S3?
Results should be uploaded to your bucket so they are available during review. See here for instructions on how to upload to your bucket: https://openscpca.readthedocs.io/en/latest/software-platforms/aws/working-with-s3-buckets/
What types of results does your code produce (e.g., table, figure)?
What is your summary of the results?
Provide directions for reviewers
Initial commit
What are the software and computational requirements needed to be able to run the code in this PR?
Nothing but local machine and R.
Are there particularly areas you'd like reviewers to have a close look at?
Is there anything that you want to discuss further?
Author checklists
Check all those that apply. Note that you may find it easier to check off these items after the pull request is actually filed.
Analysis module and review
README.mdhas been updated to reflect code changes in this pull request.Reproducibility checklist
Dockerfile.environment.ymlfile.renv.lockfile.